Molecular phylogenetics of a protein repair methyltransferase

Comparative Biochemistry and Physiology - B Biochemistry and Molecular Biology

Volumn 117, Issue 3, 1997, Pages 379-385

  Kagan, Ron M ^a   McFadden, Helen J ^b   McFadden, Philip N ^b   O'Connor, Clare ^c   Clarke, Steven ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b OREGON STATE UNIVERSITY   (United States)

^c BOSTON COLLEGE   (United States)

Author keywords

Arabidopsis thaliana; Caenorhabditis elegans; Evolution; L isoaspartyle methyltransferase; Molecular clock; Phylogenetics; Protein repair; Protein sequence comparison

Indexed keywords

ASPARTIC ACID; PROTEIN METHYLTRANSFERASE;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; BACTERIUM; CAENORHABDITIS ELEGANS; EVOLUTION; FISH; GENETIC CONSERVATION; HUMAN; INSECT; MAMMAL; MOLECULAR GENETICS; NEMATODE; NONHUMAN; PHYLOGENY; PLANT; PRIORITY JOURNAL; SEQUENCE HOMOLOGY;

ANIMALIA; ARABIDOPSIS THALIANA; BACTERIA (MICROORGANISMS); CAENORHABDITIS ELEGANS; INSECTA; MAMMALIA; NEMATODA;

EID: 0030879079     PISSN: 03050491     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0305-0491(96)00333-1     Document Type: Article

References (42)

1. Aswad, D.W.; Johnson, B.A. The unusual substrate specificity of eukaryotic protein carboxyl methyltransferases. Trends Biochem. Sci. 12:155-158;1987.
2. Brennan, T.V.; Anderson, J.W.; Jia, Z.; Waygood, E.B.; Clarke, S. Repair of spontaneously deamidated HPr phosphocarrier protein catalyzed by the L-isoaspartate-(D-aspartate) O-methyltransferase. J. Biol. Chem. 269:24586-24595;1994.
3. Carroll, R.L. Vertebrate Paleontology and Evolution. New York: Freeman; 1988.
4. Cedergren, R.; Gray, M.W.; Abel, Y.; Sankoff, D. The evolutionary relationships among known life forms. J. Mol. Evol. 28:98-112;1988.
5. Clarke, S. Protein carboxyl methyltransferases: Two distinct classes of enzymes. Annu. Rev. Biochem. 54:479-506;1985.
6. Davidson, E.H.; Peterson, K.J.; Cameron, R.A. Origin of bilaterian body plans: Evolution of developmental regulatory mechanisms. Science 270:1319-1325;1995.
7. Dickerson, R.E. The structures of cytochrome c and the rates of molecular evolution. J. Mol. Evol. 1:26-45;1971.
8. Doolittle, R.F.; Anderson, K.L.; Feng, D.F. Estimating the prokaryote-eukaryote divergence time from protein sequences. In: Femholm, B.; Bremer, K.; Jornvall, H. (eds). The Hierarchy of Life. Amsterdam: Elsevier Science Publishers B.V; 1989:73-85.
9. Doolittle, R.F.; Feng, D.-F; Tsang, S.; Cho, G.; Little, E. Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 271:470-476;1996.
10. Felsenstein, J. "PHYLIP (Phylogeny Inference Package)" version 3.56c. Distributed by the author, Dept. of Genetics, University of Washington, Seattle, WA; 1993.
11. Galletti, P.; Ingrosso, D.; Manna, C.; Clemente, G.; Zappia, V. Protein damage and methylation-mediated repair in the erythrocyte. Biochem. J. 306:313-325;1995.
12. Ghosh, A.K. Protein carboxyl methylation in the mushroom Volvariella volvacea. Phytochem. 32:1093-1096;1993.
13. Gillespie, J.H. The Causes of Molecular Evolution. New York: Oxford University Press; 1991.
14. Goffeau, A.; Barrell, B.G.; Bussey, H.; Davis, R.W.; Dujon, B.; Feldmann, H.; Galibert, F.; Hoheisel, J.D.; Jacq, C.; Johnston, M.; Louis, E.J.; Mewes, H.W.; Murakami, Y.; Philippsen, P.; Tettelin, H.; Oliver, S.G. Life with 6000 genes. Science 274:546-567;1996.
15. Johnson, B.A.; Langmack, E.L.; Aswad, D.W. Partial repair of deamidation-damaged calmodulin by protein carboxyl methyltransferase. J. Biol. Chem. 262:12283-12287;1987.
16. Johnson, B.A.; Murray, E.J., Jr.; Clarke, S.; Glass, D.B.; Aswad, D.W. Protein carboxyl methyltransferase facilitates conversion of atypical L-isoaspartyl peptides to normal L-aspartyl peptides. J. Biol. Chem. 262:5622-5629;1987.
17. Johnson, B.A.; Ngo, S.Q.; Aswad, D.W. Widespread phylogenetic distribution of a protein methyltransferase that modifies L-isoaspartyl residues. Biochem. Int. 24:841-847;1991.
18. Kagan, R.M.; Clarke, S. Widespread occurrence of three sequence motifs in diverse S-adenosylmethionine-dependent methyltransferases suggests a common structure for these enzymes. Arch. Biochem. Biophys. 310:417-427;1994.
19. Kagan, R.M.; Clarke, S. Protein L-isoaspartyl methyltransferase from the nematode Caenorhabditis elegans: genomic structure and substrate specificity. Biochemistry 34:10794-10806; 1995.
20. Kemmerer, E.C.; Lei, M.; Wu, R. Structure and molecular evolutionary analysis of a plant cytochrome c gene: Surprising implications for Arabidopsis thaliana. J. Mol. Evol. 32:227-237; 1991.
21. Kimura, M. The Neutral Theory of Molecular Evolution. New York: Cambridge University Press; 1983.
22. Ladino, C.A.; O'Connor, C.M. Methylation of atypical protein aspartyl residues during the stress response of HeLa cells. J. Cell Physiol. 153:297-304;1992.
23. Li, C.; Clarke, S. Distribution of an L-isoaspartyl protein methyltransferase in eubacteria. J. Bacteriol. 174:355-361; 1992.
24. Li, C.; Clarke, S. A protein methyltransferase specific for altered aspartyl residues is important in Escherichia coli stationary-phase survival and heat-shock resistance. Proc. Natl. Acad. Sci. USA 89:9885-9889;1992.
25. Li, W.H.; Grauer, D. Fundamentals of Molecular Evolution. Sunderland, MA: Sinauer Associates; 1991.
26. Lindquist, J.A.; McFadden, P.N. Automethylation of protein (D-aspartyl/L-isoaspartyl) carboxyl methyltransferase, a response to enzyme aging. J. Protein Chem. 13:23-30;1994.
27. Lowenson, J.D.; Clarke, S. Structural elements affecting the recognition of L-isoaspartyl residues by the L-isoaspartyl/D-aspartyl protein methyltransferase. Implications for the repair hypothesis. J. Biol. Chem. 266:19396-19406;1991.
28. Lowenson, J.D.; Clarke, S. Recognition of D-aspartyl residues in polypeptides by the erythrocyte L-isoaspartyl/D-aspartyl protein methyltransferase. Implications for the repair hypothesis. J. Biol. Chem. 267:5985-5995;1992.
29. Martin, W.; Lydiate, D.; Brinkmann, H.; Forkmann, G.; Saedler, H.; Cerff, R. Molecular phylogenies in angiosperm evolution. Mol. Biol. Evol. 10:140-162;1993.
30. McFadden, P.N.; Clarke, S. Conversion of isoaspartyl peptides to normal peptides: Implications for the cellular repair of damaged proteins. Proc. Natl. Acad. Sci. USA 84:2595-2599; 1987.
31. Mudgett, M.B.; Clarke, S. Characterization of plant L-isoaspartyl methyltransferases that may be involved in seed survival: Purification, cloning, and sequence analysis of the wheat germ enzyme. Biochemistry 32:11100-11111;1993.
32. Mudgett, M.B.; Clarke, S. A distinctly regulated protein repair L-isoaspartyl methyltransferase from Arabidopsis thaliana. Plant Mol. Biol. 30:723-737;1996.
33. Nei, M. Molecular Evolutionary Genetics. New York: Columbia University Press; 1987.
34. O'Connor, C.M.; Clarke, S. Specific recognition of altered polypeptides by widely distributed methyltransferases. Biochem. Biophys. Res. Commun. 132:1144-1150;1985.
35. O'Huigin, C.; Li, W.H. The molecular clock ticks regularly in muroid rodents and hamsters. J. Mol. Evol. 35:377-384; 1992.
36. Saccone, C.; Lanave, C.; Pesole, G. Time and biosequences. J. Mol. Evol. 37:154-159;1993.
37. Saitou, N.; Nei, M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425;1987.
38. Sarich, V.M.; Wilson, A.C. Rates of albumin evolution in primates. Proc. Natl. Acad. Sci. USA 58:142-148;1967.
39. Sarich, V.M.; Wilson, A.C. Generation time and genomic evolution in primates. Science 179:1144-1147;1973.
40. Thompson, J.D.; Higgins, D.G.; Gibson, T.J. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680;1994.
41. Vanfleteren, J.R.; Van de Peer, Y.; Blaxter, M.L.; Tweedie, S.A.; Trotman, C.; Lu, L.; Van Hauwaert, M.-L.; Moens, L. Molecular genealogy of some nematode taxa as based on cytochrome c and globin amino acid sequences. Mol. Phylogenet. Evol. 3:92-101;1994.
42. Wray, G.A.; Levinton, J.S.; Shapiro, L.H. Molecular evidence for deep Precambrian divergences among metazoan phyla. Science 274:568-573;1996.